The [claim about Flight 93 being shot down] rests largely on unsupported assertions that the main body of the engine and other large parts of the plane turned up miles from the main wreckage site — too far away to have resulted from an ordinary crash. This is incorrect, because the engine was found only 300 yards from the main crash site, and its location was consistent with the direction in which the plane had been traveling. Furthermore, the black box for the flight records the struggle onboard preceding the plane’s crash. Conspiracy theorists are left with not only an evidentially worthless theory, but also a confusing one. Why would the same U.S. government that allegedly destroyed the WTC shoot down Flight 93 before it could cause similar damage to other buildings? Of course, this question assumes a standard of logical consistency that the 9/11 Truth Movement seems to lack.
It is not well known that fighter jets scrambled to intercept Flight 93. See the account of Ben Sliney, the Federal Aviation Administration’s operations manager on September 11, 2001:
First of all, there were no military aircraft near it.
FAA headquarters never notified NORAD, in Colorado, that Flight 93 was hijacked until after it crashed at 10:03a.m. in a field in western Pennsylvania. No military plans had been scrambled in its direction.
The anomalies you mention are not relevant either.
larger than expected crater: Expected by who? How big of a crater should we have expected from an 757-222 hitting the ground upside down at a 40° angle at 563 m.p.h. with 7000 lbs of jet fuel on board?
striking lack of intact debris: 1000s of pieces of the aircraft were recovered, including parts of the planes two engines, a large piece of fuselage, the planes recorders (found in the crater) (http://www.nps.gov/flni/historyculture/upload/FAQs-long-form-July-2011.pdf). How much "intact debris" did the conspiracy theorists expect to see after a crash like this?